The ACC announced its decision Friday afternoon, saying it has issued a reprimand to the Blue Devils' leading scorer.
"The ACC considers the matter closed and will have no further comment," the league said in a brief statement.
Florida State coach Leonard Hamilton told ESPN earlier Friday that Duke coach Mike Krzyzewski called him to apologize for the incident.
"[Krzyzewski] acknowledged the fact and apologized to our staff and to let Xavier know too," Hamilton told ESPN. "We accepted it and moved on. It's the end of it.
"I was proud of the way Xavier handled it. We've done moved on. We don't want to let it become an issue. It's over.''
In video of the game broadcast, Allen was seen stretching his left foot backward near midcourt as Rathan-Mayes broke upcourt behind him in the game's final seconds. Rathan-Mayes ran into Allen's leg and stumbled to the court.
Allen then turned to Rathan-Mayes with outstretched arms, his palms facing upward.
"He wanted to keep playing physical," Allen said, according to The Fayetteville Observer. "So I tried to walk away from it as he was grabbing me. We ended up tangling up and falling."
Allen also tripped a Louisville player in Duke's victory over the Cardinals on Feb. 8 and was whistled for a flagrant foul.
Allen, who is on pace to become the ninth player in Duke history to lead the team in scoring and assists, was not called for a foul Thursday.
The sophomore guard led Duke with 18 points. Many of his points came from his drives to the basket.
ESPN's Andy Katz and C.L. Brown contributed to this report.